import_uparse: Import UPARSE file format

Description

UPARSE is an algorithm for OTU-clustering implemented within usearch.
At last check, the UPARSE algortihm was accessed via the
-cluster_otu option flag.
For details about installing and running usearch, please refer to the
usearch website.
For details about the output format, please refer to the
uparse format definition.

Usage

1
2

Arguments

upFile

(Required). A file location character string
or connection
corresponding to the file that contains the UPARSE output table.
This is passed directly to fread.
Please see its file argument documentation for further
links and details.

omitChimeras

(Optional). logical(1).
Default is TRUE.
Whether to omit entries that correspond to sequences/OTUs
that were identified as chimeras.

countTable

(Optional). logical(1).
Default is TRUE.
Whether to return the result as a wide-format table
with dimensions OTU-by-sample,
or to leave the table in its original sparse long-format
that might be more suitable for certain data.table operations.
If TRUE, entries corresponding to the same sample and OTU
have their counts summed.

OTUtable

(Optional). logical(1).
Default is TRUE.
Whether to coerce the result to otu_table format,
or leave it as a data.table format.
The former is appropriate for most phyloseq operations,
the latter is useful for a lot of custom operations
and custom ggplot2 graphics calls.

verbose

(Optional). A logical.
Default is TRUE.
Should progresss messages
be catted to standard out?

Details

Because UPARSE is an external (non-R) application, there is no direct
way to continuously check that these suggested arguments and file formats will
remain in their current state.
If there is a problem, please verify your version of usearch,
create a small reproducible example of the problem,
and post it as an issue on the
phyloseq issues tracker.